Methods of preparing quinolone analogs

ABSTRACT

The present invention relates to the preparation of compounds which are capable of inducing cell death such as apoptotic cell death (apoptosis), and/or for reducing a cell proliferative disorder.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. Ser. No. 11/499,076 filed 4Aug. 2006, which claims priority from U.S. provisional patentapplication Ser. No. 60/705,966, filed 5 Aug. 2005. The contents ofthese applications are incorporated herein by reference.

SUMMARY OF THE INVENTION

The present invention relates to methods of preparing quinolone analogs.The compounds prepared according to the methods of the present inventionmay exhibit one or more of the following activities: inhibit cellproliferation, induce cell apoptosis and stabilize a quadrupledstructure.

In one aspect, the present invention provides a method for preparing acompound having formula 1:

-   -   and pharmaceutically acceptable salts, esters and prodrugs        thereof, wherein:

A, V, and Z are independently H, halo, cyano, R², CH₂R², SR², OR² orNR¹R²; or

wherein A and Z, or V and Z may form a carbocyclic ring, heterocyclicring, aryl or heteroaryl, each of which may be optionally substitutedand/or fused with a cyclic ring;

W is NR¹R² or OR⁶ wherein R⁶ is a C₁₋₁₀ alkyl;

X is O, S, CR¹ or NR¹;

each R¹ is H or a C₁₋₆ alkyl;

each R² is H, or a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl each optionallysubstituted with a halogen, one or more non-adjacent heteroatoms, acarbocyclic ring, a heterocyclic ring, an aryl or heteroaryl, whereineach ring is optionally substituted;

R is a substituent at any position on B; and is H, OR², amino, alkoxy,amido, halogen, cyano or an inorganic substituent; or R is C₁₋₆ alkyl,C₂₋₆ alkenyl, —CONHR¹, each optionally substituted by one or morenon-adjacent heteroatoms; or two adjacent R are linked to obtain a 5-6membered optionally substituted carbocyclic or heterocyclic ring,optionally fused to an additional optionally substituted carbocyclic orheterocyclic ring;

B is an optionally substituted ring, which may be aromatic ornonaromatic, and may be monocyclic or fused with a single or multiplering, wherein said single or multiple ring may optionally contain one ormore heteroatoms;

n is 1-6;

or a compound having formula (2A) or (4A):

wherein n, V, Z, X, W, B and R are as defined in formula (1),comprising:

contacting a compound having formula (6A), (6B) or (6C)

wherein each L and L¹ is a leaving group; and A, V, and Z are as definedin formula (1);

with a compound having formula (7) and tautomers thereof

wherein n, X, B and R are as defined in formula (1); and

W is OR⁶ wherein R⁶ is a C₁₋₁₀ alkyl; or W is NR¹R², wherein R¹ and R²are as defined in formula (1);

wherein said compound having formula (6A), (6B) or (6C) is contactedwith said compound having formula (7) and tautomers thereof in thepresence of a base to produce a compound having formula (1), andoptionally hydrolyzing said compound of formula (1).

In the above method, the compound having formula (6A), (6B) or (6C) maybe contacted with a compound of formula (7) or tautomers thereof in thepresence of a base and coordinating atom, such as the coordinating metalof a Lewis acid.

In particular examples, the base is a non-nucleophilic base having a pKaof less than 20. Various bases known in the art may be used to practicethe methods of the invention, including but not limited to triethylamine(TEA), diisopropyl ethyl amine (DIEA), diazabicycloundecene (DBU),cesium carbonate, 1,8-Bis(dimethylamino)naphthalene (Proton sponge) anddimethylamino pyridine (DMAP).

Suitable Lewis acids for use in practicing the methods of the inventionmay be selected by conducting a test reaction, and observing the amountof reaction product produced, as described hereafter. In one embodiment,the Lewis acid has formula ML_(n), wherein L is a halogen atom or anorganic radical, n is 3-5, and M is a group II metal, such as MgCl₂.Other M groups include but are not limited to group III elemental atom(e.g., B), a group IV elemental atom, As, Sb, V or Fe.

In the above method, the compound having formula (1), (2A) or (4A)wherein W is OR⁶ and R⁶ is a C₁₋₆ alkyl, may further be contacted withan amine of the formula

HNR¹—(CR¹ ₂)_(n)—NR³R⁴  (3)

wherein R¹ and R³ are independently H or C₁₋₆ alkyl;

n is 1-6; and

R⁴ is H, a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl optionally containing one ormore non-adjacent heteroatoms selected from N, O and S, and optionallysubstituted with a carbocyclic or heterocyclic ring; or R³ and R⁴together with N may form an optionally substituted ring containing oneor more N, O or S.

In the above formula (3), R³ and R⁴ together with N may form anoptionally substituted piperidine, pyrrolidine, piperazine, morpholine,thiomorpholine, imidazole, or aminothiadiazole.

In the above method, the compound having formula (1), (2A) or (4A)wherein W is OR⁶ and R⁶ is a C₁₋₆ alkyl, may further be contacted withan amine of the formula HNR¹R², provided said amine is not NH₃. In theamine HNR¹R², the R¹ substituent may be H, and R² is a C₁₋₁₀ alkyloptionally substituted with a heteroatom, a C₃₋₆ cycloalkyl, aryl or a5-14 membered heterocyclic ring containing one or more N, O or S; or R¹and R² together with N may form an optionally substituted heterocyclicring containing one or more N, O or S. In one example, R² is a C₁₋₁₀alkyl substituted with morpholine, thiomorpholine, imidazole,aminothiadiazole, pyrrolidine, piperazine, pyridine or piperidine; or R¹and R² together with N form piperidine, pyrrolidine, piperazine,morpholine, thiomorpholine, imidazole, or aminothiadiazole.

In each of the above formula, B may be an optionally substituted phenyl.Furthermore, each R in the above formula may be H or halo. The Xsubstituent in each of the above formula may be NR¹ or S. In otherexamples, one of A and V in each of the above formula is H or halo, suchas a fluoro or a chloro. In each of the above formula, each Z may be H,halo, or SR² wherein R² is C₁₋₁₀ alkyl.

In the above formula (6A), (6B) or (6C), each L and L¹ is suitableleaving group such as halo, sulfonate, sulfoxide, sulfone, acyloxy,phosphonate, imidazole, benzotriazole, or imide. Other leaving groupswhich may be suitable for use in the methods of the invention includebut are not limited to tosylate, alkyl sulfonyl, carbonate, acetate,carbamate, trifluoroacetate, phosphate, methoxy or activated methoxy,nitro, boron, or a substituted boron such as boronate esters.

In the above methods, a compound having formula (6A), (6B) or (6C) maybe contacted with a compound having formula (7) to form a mixture, andfurther contacting the mixture with a base. The mixture may be cooled toa temperature below room temperature prior to addition of base.Alternatively, the base may be added to the mixture at room temperatureor at a temperature above room temperature. In particular examples, thebase is an amine, such as trialkylamine.

In one aspect, the methods of the present invention may be used toprepare a compound having formula (2B), (4), (4B) or (5A):

wherein n, W, V, A, Z, X, B and R are as defined in formula (1).

In another aspect, the present invention provides methods for preparinga compound having formula (8)

wherein V, A, Z, and Y when attached to C are independently H, halo,azido, R², CH₂R², SR², OR², NR¹R²; or absent when attached to N;

T¹, T², T³, and T are independently C, N or S;

W is NR¹R² or OR⁶, wherein R⁶ is a C₁₋₁₀ alkyl;

X is O, S, CR¹ or NR¹;

E together with N and X form a ring, which may be fused with a single ormultiple ring, wherein the single or multiple ring optionally containsone or more heteroatoms;

n is 1-6;

p is 0-1;

each R¹ is H or a C₁₋₆ alkyl;

each R² is H, or a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl each optionallysubstituted with a halogen, one or more non-adjacent heteroatoms, acarbocyclic ring, a heterocyclic ring, an aryl or heteroaryl, whereineach ring is optionally substituted;

R⁵ is a substituent at any position on E; and is H, OR², amino, alkoxy,amido, halogen, cyano or an inorganic substituent; or R is C₁₋₆ alkyl,C₂₋₆ alkenyl, —CONHR¹, each optionally substituted by one or morenon-adjacent heteroatoms; or two adjacent R⁵ are linked to obtain a 5-6membered optionally substituted carbocyclic or heterocyclic ring,optionally fused to an additional optionally substituted carbocyclic orheterocyclic ring;

comprising contacting a compound having a formula (9) with a compoundhaving formula (10) and tautomers thereof:

wherein n, V, A, Z, Y, T¹, T², T³, T⁴, X, W, E and R⁵ are as defined informula (8); and

each L and L¹ is a leaving group.

In the above method, the compound having formula (9) may be contactedwith a compound of formula (10) or tautomers thereof in the presence ofa base and coordinating atom such as the coordinating metal of a Lewisacid. Various bases and Lewis acids, such as those previously describedand which would be known to those skilled in the art, may be used.

In the above formula (8), each T¹, T², T³ and may be C. In anotherembodiment, T¹ is N, and each T², T³, and T⁴ is C. In yet anotherembodiment, T² is N, and each T¹, T³, and T⁴ is C. In other embodiments,each T¹ and T³ is N, and each T² and T⁴ is C. In another embodiment,each T¹ and T⁴ is N, and each T² and T³ is C. In yet another embodiment,each T¹, T², and T³ is CR¹, and is N.

In yet another embodiment, p in formula (8) is 0, T² and T³ are C and T⁴is S.

In the above formula (9), each L and L¹ may be halo, tosylate, alkylsulfonyl, carbonate, acetate, carbamate, trifluoroacetate, phosphate,methoxy or activated methoxy, nitro, boron, or a substituted boron suchas boronate esters. Other leaving groups which may be suitable for usein the methods of the invention include but are not limited tosulfonate, sulfoxide, sulfone, acyloxy, phosphonate, imidazole,benzotriazole, or imide. In particular embodiments, each L and L¹ ishalo.

In the above formula (10), W may be OR⁶ and R⁶ is a C₁₋₆ alkyl.Furthermore, the double bond linked to N in formula (10) may bedelocalized, and the compound may be converted to its tautomeric isomer.

In the above formula (8) and (10), E together with N may be a 5-6membered heteroaryl, or E may be selected from the group consisting of

wherein X is O, S, CR¹ or NR¹;

X¹ and X² are independently CR¹ or NR¹;

each R¹ is H or C₁₋₆ alkyl;

R and n are as defined in formula (8).

In yet another aspect, the present invention provides a method forpreparing a compound having formula (11):

and pharmaceutically acceptable salts, esters and prodrugs thereof;

wherein V, X, and Y are absent if attached to a heteroatom other thanNitrogen, and independently H, halo, azido, R², CH₂R², SR², OR² or NR¹R²when attached to C or N; or

wherein V and X, or X and Y may form a carbocyclic ring, heterocyclicring, aryl or heteroaryl, each of which may be optionally substitutedand/or fused with a cyclic ring;

Z¹, Z² and Z³ are C, N, O or S;

Z is O, S, NR², CH₂ or C═O;

E together with N and Z forms an optionally substituted 5- or 6-memberedring that is fused to an optionally substituted aryl or heteroaryl,wherein said aryl or heteroaryl may be monocyclic or fused with a singleor multiple ring, and wherein said single or multiple ring optionallycontains one or more heteroatoms;

U is R², OR², NR¹R², NR¹—(CR¹ ₂)_(n)—NR³R², SO₃R², SO₂NR¹R² orSO₂NR¹—(CR¹ ₂)_(n)—NR³R⁴;

wherein in each NR¹R², R¹ and R² together with N may form an optionallysubstituted ring;

in NR³R⁴, R³ and R⁴ together with N may form an optionally substitutedring;

R¹ and R³ are independently H or C₁₋₆ alkyl;

each R² is H, or a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl each optionallysubstituted with a halogen, one or more non-adjacent heteroatomsselected from N, O and S, a carbocyclic ring, a heterocyclic ring, anaryl or heteroaryl, wherein each ring is optionally substituted; or R²is an optionally substituted carbocyclic ring, heterocyclic ring, arylor heteroaryl; or R² is COR¹ or S(O)_(x)R¹ wherein x is 1-2;

R⁴ is H, a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl optionally containing one ormore non-adjacent heteroatoms selected from N, O and S, and optionallysubstituted with a carbocyclic or heterocyclic ring; or R³ and R⁴together with N may form an optionally substituted ring;

each R⁵ is a substituent at any position on W; and is H, OR², amino,alkoxy, amido, halogen, cyano or an inorganic substituent; or R⁵ is C₁₋₆alkyl, C₂₋₆ alkenyl, —CONHR¹, each optionally substituted by halo,carbonyl or one or more non-adjacent heteroatoms; or two adjacent R⁵ arelinked to obtain a 5-6 membered optionally substituted carbocyclic orheterocyclic ring, optionally fused to an additional optionallysubstituted carbocyclic or heterocyclic ring; and

n is 1-6.

In the above formula (11), ring T may form an optionally substituted5-membered ring selected from the group consisting of:

In the above formula (11), E together with N and Z may form a 5- or6-membered ring that is fused to a phenyl, or E may be selected from thegroup consisting of

wherein X is O, S, CR¹ or NR¹;

X¹ and X² are independently CR¹ or NR¹;

each R¹ is H or C₁₋₆ alkyl;

R and n are as defined in formula (8).

In one embodiment, the methods of the invention may be used to preparecompounds having general formula (12A) or (12B):

wherein U, V, E, X, y, Z, Z¹, Z², Z³, R⁵ and n are as described informula (11);

Z⁴ is CR⁶, NR², or C═O; and

Z and Z⁴ may optionally form a double bond.

In yet another embodiment, the methods of the invention may be used toprepare compounds having general formula (13), (14) and (15)

wherein U, V, X, Y, Z, Z¹, Z², Z³, R⁵ and n are as described in formula(11).

The compounds prepared according to the methods of the present inventionare useful for ameliorating a cell proliferative disorder such as atumor or a cancer; or are intermediates to such compounds. The cancermay be pancreatic cancer, including non-endocrine and endocrine tumors.Illustrative examples of non-endocrine tumors include but are notlimited to adenocarcinomas, acinar cell carcinomas, adenosquamouscarcinomas, giant cell tumors, intraductal papillary mucinous neoplasms,mucinous cystadenocarcinomas, pancreatoblastomas, serous cystadenomas,solid and pseudopapillary tumors. An endocrine tumor may be an isletcell tumor.

The compounds prepared according to the methods of the present inventionare also useful for reducing cell proliferation and/or inducing celldeath, such as apoptosis or apoptotic cell death, in a system or asubject; or are intermediates to such compounds. The system may be acell or a tissue. In one embodiment, the system includes a pancreaticcell, such as a cell from a subject or a cultured cell (e.g., in vitroor ex vivo). In particular embodiments, the system includes a pancreaticcancer cell. In one embodiment, the system is a cell line such as PC3,HCT116, HT29, MIA Paca-2, HPAC, Hs700T, Panc10.05, Panc 02.13, PL45, SW190, Hs 766T, CFPAC-1 and PANC-1. The subject may be human or animal.Furthermore, the compounds prepared according to the methods of thepresent invention are useful for reducing microbial titers and/or forameliorating a microbial infection; or are intermediates to suchcompounds. The microbial titers may be viral, bacterial or fungaltiters.

DEFINITIONS

As used herein, the term “alkyl” refers to a carbon-containing compound,and encompasses groups containing one or more heteroatoms. The term“alkyl” also encompasses alkyls substituted with one or moresubstituents including but not limited to OR¹, amino, amido, halo, ═O,aryl, heterocyclic groups, or inorganic substituents.

As used herein, the term “carbocycle” refers to a cyclic compoundcontaining only carbon atoms in the ring, whereas a “heterocycle” refersto a cyclic compound comprising a heteroatom. The carbocyclic andheterocyclic structures encompass compounds having monocyclic, bicyclicor multiple ring systems.

As used herein, the term “aryl” refers to a polyunsaturated, typicallyaromatic hydrocarbon substituent, whereas a “heteroaryl” or“heteroaromatic” refer to an aromatic ring containing at least oneheteroatom selected from N, O and S. The aryl and heteroaryl structuresencompass compounds having monocyclic, bicyclic or multiple ringsystems.

As used herein, the term “heteroatom” refers to any atom that is notcarbon or hydrogen, such as nitrogen, oxygen or sulfur.

Illustrative examples of heterocycles include but are not limited totetrahydrofuran, 1,3-dioxolane, 2,3-dihydrofuran, pyran,tetrahydropyran, benzofuran, isobenzofuran, 1,3-dihydro-isobenzofuran,isoxazole, 4,5-dihydroisoxazole, piperidine, pyrrolidine,pyrrolidin-2-one, pyrrole, pyridine, pyrimidine,octahydro-pyrrolo[3,4-b]pyridine, piperazine, pyrazine, morpholine,thiomorpholine, imidazole, imidazolidine-2,4-dione,1,3-dihydrobenzimidazol-2-one, indole, thiazole, benzothiazole,thiadiazole, thiophene, tetrahydro-thiophene 1,1-dioxide, diazepine,triazole, guanidine, diazabicyclo[2.2.1]heptane,2,5-diazabicyclo[2.2.1]heptane, 2,3,4,4a,9,9a-hexahydro-1H-β-carboline,oxirane, oxetane, tetrahydropyran, dioxane, lactones, aziridine,azetidine, piperidine, lactams, and may also encompass heteroaryls.Other illustrative examples of heteroaryls include but are not limitedto furan, pyrrole, pyridine, pyrimidine, imidazole, benzimidazole andtriazole.

As used herein, the term “Lewis acid” refers to any species that canaccept an electron pair, such as metal ions and electron-deficientmolecules. In one example, the methods of the present invention use aLewis acid such as magnesium chloride. Other Lewis acids may be used inpracticing the methods of the present invention, including specieshaving the formula ML_(n), wherein L is a halogen atom or an organicradical such as an alkyl group, n is 3-5, and M is a group III elementalatom (e.g., B, Al, Ga, In), or a group IV elemental atom (e.g., Zr, Ti,Sn). Strong Lewis acidity is also observed for certain group V elementalatoms (e.g., As, Sb, V), and group VIII elemental atoms (e.g., Fe).Group II elemental atoms (e.g., Zn, Cd) generally display moderate Lewisacidity. Particular Lewis acids that may be used to practice the methodsof the present invention include but are not limited to: MgL₂; BL₃;AlL₃; FeL₃; GaL₃; SbL₅; InL₃; ZrL₄; SnL₄; TiL₄; TiL₃; AsL₃; SbL₃. (See,e.g., D. P. N. Satchell & R. S. Satchell, Quantitative Aspects of theLewis Acidity of Covalent Metal Halides and their Organo Derivatives, 69CHEM. REV. 251, 253-55 (1969)).

As used herein, the term “apoptosis” refers to an intrinsic cellself-destruction or suicide program. In response to a triggeringstimulus, cells undergo a cascade of events including cell shrinkage,blebbing of cell membranes and chromatic condensation and fragmentation.These events culminate in cell conversion to clusters of membrane-boundparticles (apoptotic bodies), which are thereafter engulfed bymacrophages.

DESCRIPTION OF THE INVENTION

The present invention relates to the preparation of compounds having anyone of formula (1), (2A), (2B), (4), (4A), (4B), (5A), (5B), (8), (11),(12A), (12B) and 13-15 and pharmaceutically acceptable salts, esters,and prodrugs thereof. The compounds may interact with regions of DNAthat can form quadruplexes, and may also be used for treatment of cellproliferative disorders.

In one aspect, the present invention provides a method for preparing acompound having formula 1:

and pharmaceutically acceptable salts, esters and prodrugs thereof,wherein:

A, V, and Z are independently H, halo, cyano, R², CH₂R², SR², OR² orNR¹R²; or

wherein A and Z, or V and Z may form a carbocyclic ring, heterocyclicring, aryl or heteroaryl, each of which may be optionally substitutedand/or fused with a cyclic ring;

W is NR¹R² or OR⁶ wherein R⁶ is a C₁₋₁₀ alkyl;

X is O, S, CR¹ or NR¹;

each R¹ is H or a C₁₋₆ alkyl;

each R² is H, or a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl each optionallysubstituted with a halogen, one or more non-adjacent heteroatoms, acarbocyclic ring, a heterocyclic ring, an aryl or heteroaryl, whereineach ring is optionally substituted;

R is a substituent at any position on B; and is H, OR², amino, alkoxy,amido, halogen, cyano or an inorganic substituent; or R is C₁₋₆ alkyl,C₂₋₆ alkenyl, —CONHR¹, each optionally substituted by one or morenon-adjacent heteroatoms; or two adjacent R are linked to obtain a 5-6membered optionally substituted carbocyclic or heterocyclic ring,optionally fused to an additional optionally substituted carbocyclic orheterocyclic ring;

B is an optionally substituted ring, which may be aromatic ornonaromatic, and may be monocyclic or fused with a single or multiplering, wherein said single or multiple ring may optionally contain one ormore heteroatoms;

n is 1-6;

or a compound having formula (2A) or (4A):

wherein n, V, Z, X, W, B and R are as defined in formula (1),comprising:

-   -   contacting a compound having formula (6A), (6B) or (6C)

-   -   wherein each L and L¹ is a leaving group; and A, V, and Z are as        defined in formula (1);    -   with a compound having formula (7) and tautomers thereof

-   -   wherein n, X, B and R are as defined in formula (1); and

W is OR⁶ wherein R⁶ is a C₁₋₁₀ alkyl; or W is NR²R¹, wherein R¹ and R²are as defined in formula (1);

wherein said compound having formula (6A), (6B) or (6C) is contactedwith said compound having formula (7) and tautomers thereof in thepresence of a base to produce a compound having formula (1), andoptionally hydrolyzing said compound of formula (1).

In another aspect, the present invention provides methods for preparinga compound having formula (8)

wherein V, A, Z, and Y when attached to C are independently H, halo,azido, R², CH₂R², SR², OR², NR¹R²; or absent when attached to N;

T¹, T², T³, and T⁴ are independently C, N or S;

W is NR¹R² or OR⁶, wherein R⁶ is a C₁₋₁₀ alkyl;

X is O, S, CR¹ or NR¹;

E together with N and X form a ring, which may be fused with a single ormultiple ring, wherein the single or multiple ring optionally containsone or more heteroatoms;

n is 1-6;

p is 0-1;

each R¹ is H or a C₁₋₆ alkyl;

each R² is H, or a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl each optionallysubstituted with a halogen, one or more non-adjacent heteroatoms, acarbocyclic ring, a heterocyclic ring, an aryl or heteroaryl, whereineach ring is optionally substituted;

R⁵ is a substituent at any position on E; and is H, OR², amino, alkoxy,amido, halogen, cyano or an inorganic substituent; or R is C₁₋₆ alkyl,C₂₋₆ alkenyl, —CONHR¹, each optionally substituted by one or morenon-adjacent heteroatoms; or two adjacent R⁵ are linked to obtain a 5-6membered optionally substituted carbocyclic or heterocyclic ring,optionally fused to an additional optionally substituted carbocyclic orheterocyclic ring;

comprising contacting a compound having a formula (9) with a compoundhaving formula (10) and tautomers thereof:

wherein n, V, A, Z, Y, T¹, T², T³, T⁴, X, W, E and R⁵ are as defined informula (8); and

each L and L¹ is a leaving group.

In the above methods, the reagents in the presence of a base andcoordinating atom, such as the coordinating atom of a Lewis acid.Although the mechanism is not necessary to practice the invention, theuse of a co-ordinating metal or acid allows the hydrogen on the α-carbonin formula (7) and (10) to become more acidic, thus facilitating itsremoval by a weak base (in this case a trialkylamine base). Hence theanion (reactive intermediate) can be generated under more mildconditions and reacted with the other reactant. The coordinating metalthen orientates (holds) the resulting products in a conformation whichfacilitates the second bond formation allowing it to occur under milderconditions. In this step, again the remaining hydrogen on the α-carbonis rendered more acidic, and the molecule is in a conformation in whichthe reactive atoms are held more closely together, helping overcomeentropic barriers.

The compounds of the present invention having formula (1), (2A), (2B),(4), (4A), (4B), (5A), (5B), (8), (11), (12A), (12B) and 13-15 arereproduced below:

wherein each substituent is as defined above.

In the above formula (4), X may be NR¹;

A and V may independently be H or halo;

Z may be an optionally substituted carbocyclic ring, heterocyclic ring,aryl, or heteroaryl; and R may be a substituent at any position on thefused ring; and is H, OR², cyano, halo, or an inorganic substituent; orC₁₋₆ alkyl, C₂₋₆ alkenyl, C₃₋₇ cycloalkyl, each optionally substitutedby halo, ═O or one or more heteroatoms.

In the above formula (4), Z may be a 5-6 membered heterocyclic ringcontaining N, O, or S, and optionally substituted with halo, alkyl,alkoxy, or acetyl.

In each of the above formula, ring B in formula (1), (2A), (2B), (4A),(7) or (8), or ring E in formula (11), (12A) and (12B) may be selectedfrom the group consisting of:

wherein each Q, Q¹, Q², and Q³ is independently CH or N;

Y is independently O, CH, C═O or NR¹;

R¹ is as defined in formula (1); and

R⁵ is a substituent at any position on ring B or E; and is H, OR²,amino, alkoxy, amido, halogen, cyano or an inorganic substituent; or Ris C₁₋₆ alkyl, C₂₋₆ alkenyl, —CONHR¹, each optionally substituted by oneor more non-adjacent heteroatoms; or two adjacent R⁵ are linked toobtain a 5-6 membered optionally substituted carbocyclic or heterocyclicring, optionally fused to an additional optionally substitutedcarbocyclic or heterocyclic ring.

In one embodiment, B or E is an optionally substituted phenyl. Inparticular examples, each R⁵ in each of the above formula is H or halo.

In each of the above formula, one of A (if present) or V may be H orhalo. In particular examples, one of A or V may be H or fluoro.

In each of the above formula, Z may be H, halo, or SR², wherein R² is aC₁₋₁₀ alkyl or C₂₋₁₀ alkenyl optionally substituted with a heteroatom, acarbocyclic ring, a heterocyclic ring, an aryl or a heteroaryl. In oneexample, R² is a C₁₋₁₀ alkyl.

In each of the above formula, X may be NR¹ or S.

In some embodiments, Z, A, and V in each of the above formula may beindependently H. In other embodiments, two of A, Z and V are H, andsometimes only one of A, Z and V is H. In certain embodiments, only oneof A, Z and V is a halogen (e.g., fluorine), and sometimes two of A, Zand V are halogen. In other embodiments, Z, A and V in each of the aboveformula is SR², which may be oxidized to SO₂R, which can readily bereplaced with another nucleophile, such as OR or an amino group.

In some embodiments, W is OR⁶ group, which may be replaced with a—R⁷R⁸—(CH₂)_(n)—CHR²—NR³R⁴, wherein R⁷ is N or CR¹ wherein R¹ is H orC₁₋₆ alkyl; R⁸ is H or C₁₋₁₀ alkyl, and wherein in the —CHR²—NR³R⁴moiety, one of R³ or R⁴ together with the C may form an optionallysubstituted heterocyclic or heteroaryl ring, or wherein in the—CHR²—NR³R⁴ moiety each R³ or R⁴ together with the N may form anoptionally substituted carbocyclic, heterocyclic, aryl or heteroarylring. In some embodiment, W is not NH₂.

In each of the above formula, one, two, three or all of V, Z, and A (ifpresent) may independently be selected from a NR¹R² moiety, wherein R¹is H, and R² is a C₁₋₁₀ alkyl optionally substituted with a heteroatom,a C₃₋₆ cycloalkyl, aryl or a 5-14 membered heterocyclic ring containingone or more N, O, or S. In some embodiments, W is a NR¹R² moiety and oneof A or Z is the same or a different NR¹R² moiety compared to W. If morethan one NR¹R² moiety is present in a compound within the invention, aswhen both A and W are NR¹R² in a compound according to formula (1), forexample, each R¹ and each R² are independently selected.

In one example, R² is a C₁₋₁₀ alkyl substituted with an optionallysubstituted 5-14 membered heterocyclic ring. For example, R² may be aC₁₋₁₀ alkyl substituted with morpholine, thiomorpholine, imidazole,aminothiadiazole, pyrrolidine, piperazine, pyridine or piperidine.Alternatively, R¹ and R² together with N may form an optionallysubstituted heterocyclic ring containing one or more N, O, or S. Forexample, R¹ and R² together with N may form piperidine, pyrrolidine,piperazine, morpholine, thiomorpholine, imidazole, or aminothiadiazole.

Illustrative examples of optionally substituted heterocyclic ringsinclude but are not limited to tetrahydrofuran, 1,3-dioxolane,2,3-dihydrofuran, tetrahydropyran, benzofuran, isobenzofuran,1,3-dihydro-isobenzofuran, isoxazole, 4,5-dihydroisoxazole, piperidine,pyrrolidine, pyrrolidin-2-one, pyrrole, pyridine, pyrimidine,octahydro-pyrrolo[3,4-b]pyridine, piperazine, pyrazine, morpholine,thiomorpholine, imidazole, aminothiadiazole, imidazolidine-2,4-dione,benzimidazole, 1,3-dihydrobenzimidazol-2-one, indole, thiazole,benzothiazole, thiadiazole, thiophene, tetrahydro-thiophene 1,1-dioxide,diazepine, triazole, diazabicyclo[2.2.1]heptane,2,5-diazabicyclo[2.2.1]heptane, and2,3,4,4a,9,9a-hexahydro-1H-β-carboline.

In each of the above formula, each optionally substituted moiety may besubstituted with one or more halo, OR², NR¹R², carbamate, C₁₋₁₀ alkyl,C₂₋₁₀ alkenyl, each optionally substituted by halo, C═O, aryl or one ormore heteroatoms; inorganic substituents, aryl, carbocyclic or aheterocyclic ring.

The compounds of the present invention may be chiral. As used herein, achiral compound is a compound that is different from its mirror image,and has an enantiomer. Furthermore, the compounds may be racemic, or anisolated enantiomer or stereoisomer. Methods of synthesizing chiralcompounds and resolving a racemic mixture of enantiomers are well knownto those skilled in the art. See, e.g., March, “Advanced OrganicChemistry,” John Wiley and Sons, Inc., New York, (1985), which isincorporated herein by reference.

Illustrative examples of compounds which may be prepared using themethods of the invention are shown in Table 1, and in the Examples. Thepresent invention also encompasses other compounds having any one of theformula (1), (2), (2A), (2B), (4), (4A), (4B), (5A), (5B), (8), (11),(12A), (12B) and 13-15 comprising substituents V, A, Z, Y, and Windependently selected from the substituents exemplified in Table 1 andin the Examples. Thus, the present invention is not limited to thespecific combination of substituents described in various embodimentsbelow.

TABLE 1 MS Yield:

325.3 77%

359.3(M + H)⁺ 76%

369.3(M + H)⁺ 62%

359.3(M + H)⁺ 90%(2:1 mix)

411.2(M + H)⁺ 56%

356.3(M + H)⁺ 92%

356.4(M + H)⁺ 90%

392.2(M + H)⁺ 95%

372.1(M + H)⁺ 98%

392.2(M + H)⁺ 90%

411.3(M + H)⁺ 76%

394.4 60%

289.2 84%

409.3 89%

377.4 68%

353.2 12%

377.3 97%

306.7 10%

381.0 68%

392.2 97%

342.2 41%

390   73%

424.1 43%

438.6 62%

374.5 45%

364.2 56%

363.2 34%

330.0 44%

313.1 29%

The compounds described herein may interact with regions of DNA that canform quadruplexes; or are useful intermediates to such compounds.Because regions of DNA that can form quadruplexes are regulators ofbiological processes such as oncogene transcription, modulators ofquadruplex biological activity can be utilized as cancer therapeutics.Molecules that interact with regions of DNA that can form quadruplexescan exert a therapeutic effect on certain cell proliferative disordersand related conditions. Particularly, abnormally increased oncogeneexpression can cause cell proliferative disorders, and quadruplexstructures typically down-regulate oncogene expression. Examples ofoncogenes include but are not limited to MYC, HIF, VEGF, ABL, TGF,PDGFA, MYB, SPARC, HUMTEL, HER, VAV, RET, H-RAS, EGF, SRC, BCL1, BCL2,DHFR, HMGA, and other oncogenes known to one of skill in the art.Furthermore, the compounds described may induce cell death (e.g.,apoptosis) and not interact with regions of DNA that can formquadruplexes; or are useful intermediates to such compounds.

Molecules that bind to regions of DNA that can form quadruplexes canexert a biological effect according to different mechanisms, whichinclude for example, stabilizing a native quadruplex structure,inhibiting conversion of a native quadruplex to duplex DNA by blockingstrand cleavage, and stabilizing a native quadruplex structure having aquadruplex-destabilizing nucleotide substitution and other sequencespecific interactions. Thus, compounds that bind to regions of DNA thatcan form quadruplexes described herein may be administered to cells,tissues, or organisms for the purpose of down-regulating oncogenetranscription and thereby treating cell proliferative disorders.

Determining whether the biological activity of native DNA that can formquadruplexes is modulated in a cell, tissue, or organism can beaccomplished by monitoring quadruplex biological activity. Quadruplexforming regions of DNA biological activity may be monitored in cells,tissues, or organisms, for example, by detecting a decrease or increaseof gene transcription in response to contacting the quadruplex formingDNA with a molecule. Transcription can be detected by directly observingRNA transcripts or observing polypeptides translated by transcripts,which are methods well known in the art.

Molecules that interact with quadruplex forming DNA and quadruplexforming nucleic acids can be utilized to treat many cell proliferativedisorders. Cell proliferative disorders include, for example, colorectalcancers and hematopoietic neoplastic disorders (i.e., diseases involvinghyperplastic/neoplastic cells of hematopoietic origin such as thosearising from myeloid, lymphoid or erythroid lineages, or precursor cellsthereof). The diseases can arise from poorly differentiated acuteleukemias, e.g., erythroblastic leukemia and acute megakaryoblasticleukemia. Additional myeloid disorders include, but are not limited to,acute promyeloid leukemia (APML), acute myelogenous leukemia (AML) andchronic myelogenous leukemia (CML) (Vaickus, Crit. Rev. inOncol./Hemotol. 11:267-297 (1991)). Lymphoid malignancies include, butare not limited to acute lymphoblastic leukemia (ALL), which includesB-lineage ALL and T-lineage ALL, chronic lymphocytic leukemia (CLL),prolymphocytic leukemia (PLL), hairy cell leukemia (HLL) andWaldenstrom's macroglobulinemia (WM). Additional forms of malignantlymphomas include, but are not limited to non-Hodgkin lymphoma andvariants thereof, peripheral T cell lymphomas, adult T cellleukemia/lymphoma (ATL), cutaneous T-cell lymphoma (CTCL), largegranular lymphocytic leukemia (LGF), Hodgkin's disease andReed-Sternberg disease. Cell proliferative disorders also includecancers of the colorectum, breast, lung, liver, pancreas, lymph node,colon, prostate, brain, head and neck, skin, liver, kidney, and heart.Compounds that interact with regions of DNA that may form quadruplexesalso can be utilized to target cancer related processes and conditions,such as increased angiogenesis, by inhibiting angiogenesis in a subject.

Compounds that interact with quadruplex forming regions of DNA can alsobe used to reduce a microbial infection, such as a viral infection.Retroviruses offer a wealth of potential targets for G-quadruplextargeted therapeutics. G-quadruplex structures have been implicated asfunctional elements in at least two secondary structures formed byeither viral RNA or DNA in HIV, the dimer linker structure (DLS) and thecentral DNA flap (CDF). Additionally, DNA aptamers which are able toadopt either inter- or intramolecular quadruplex structures are able toinhibit viral replication. In one example, DNA aptamers are able toinhibit viral replication by targeting the envelope glycoprotein(putatively). In another example, DNA aptamers inhibit viral replicationby targeting the HIV-integrase respectively, suggesting the involvementof native quadruplex structures in interaction with the integraseenzyme.

Dimer linker structures, which are common to all retroviruses, serve tobind two copies of the viral genome together by a non-covalentinteraction between the two 5′ ends of the two viral RNA sequences. Thegenomic dimer is stably associated with the gag protein in the maturevirus particle. In the case of HIV, the origin of this non-covalentbinding may be traced to a 98 base-pair sequence containing several runsof at least two consecutive guanines (e.g., the 3′ for the formation ofRNA dimers in vitro). An observed cation (potassium) dependence for theformation and stability of the dimer in vitro, in addition to thefailure of an antisense sequence to effectively dimerize, has revealedthe most likely binding structure to be an intermolecular G-quadruplex.

Prior to integration into the host genome, reverse transcribed viral DNAforms a pre-integration complex (PIC) with at least two major viralproteins, integrase and reverse transcriptase, which is subsequentlytransported into the nucleus. The Central DNA Flap (CDF) refers to99-base length single-stranded tail of the + strand, occurring near thecenter of the viral duplex DNA, which is known to a play a role in thenuclear import of the PIC. Oligonucleotide mimics of CDF are known toform intermolecular G-quadruplex structures in cell-free systems.

Thus, compounds that recognize quadruplex forming regions can be used tostabilize the dimer linker structure and thus prevent de-coupling of thetwo RNA strands. Also, by binding to the quadruplex structure formed bythe CDF, protein recognition and/or binding events for nuclear transportof the PIC may be disrupted. In either case, a substantial advantage canexist over other anti-viral therapeutics. Current Highly ActiveAnti-Retroviral Therapeutic (HAART) regimes rely on the use ofcombinations of drugs targeted towards the HIV protease and HIVintegrase. The requirement for multi-drug regimes is to minimize theemergence of resistance, which will usually develop rapidly when agentsare used in isolation. The source of such rapid resistance is theinfidelity of the reverse transcriptase enzyme which makes a mutationapproximately once in every 10,000 base pairs. An advantage of targetingviral quadruplex structures over protein targets, is that thedevelopment of resistance is slow or is impossible. A point mutation ofthe target quadruplex can compromise the integrity of the quadruplexstructure and lead to a non-functional copy of the virus. A singletherapeutic agent based on this concept may replace the multiple drugregimes currently employed, with the concomitant benefits of reducedcosts and the elimination of harmful drug/drug interactions.

The following examples are offered to illustrate but not to limit theinvention.

EXAMPLE 1

Ethyl 2-(benzothiazol-2-yl)acetate was prepared by the method ofAbbotto, Bradamante et. al. (J. Org. Chem. 2002, 16, 5753). A neatmixture of 2-aminothiophenol (6.94 g, 50 mmol) and ethyl cyanoacetate(5.65 g, 50 mmol) was heated at 120° C. for 3 hours at which time TLCanalysis indicated that the reaction was complete as judged by thedisappearance of starting material. The dark orange mixture was dilutedwith ethyl acetate/hexanes and purified by flash chromatography using10-20% ethyl acetate/hexanes (Rf=0.35, 10% ethyl acetate/hexanes) as aneluant. After concentration by rotary evaporator, ethyl2-(benzothiazol-2-yl)acetate could be obtained as a yellow oil in 72%yield (7.97 g).

LCMS: 222.3 (M+H)⁺.

2,6-dichloropicolinic acid (2.70 g, 11 mmol) was suspended indichloromethane (10 mL) and treated with oxalyl chloride (1.74 g, 14mmol). The mixture was cooled in an ice bath and 2 drops ofdimethylformamide was added. After an initial vigorous outgassing, theice bath was removed and the solution was stirred for 18 hours at roomtemperature. An aliquot was quenched with methanol and analyzed by LCMSindicating that all the acid had been converted to the acid chloride.The solution was concentrated on a rotary evaporator to give the acidchloride as a light brown crystalline solid which was used in thesubsequent step without further purification. LCMS: 206.2 (methyl esterM+H)⁺.

Tetrahydrofuran (25 mL) was added to a mixture of ethyl2-(benzothiazol-2-yl)acetate, magnesium chloride (2.21 g, 10 mmol) and2,6-dichloropicolinyl chloride (11 mmol). The resulting suspension wascooled in an ice bath and triethylamine (2.02 g, 20 mmol) was addeddropwise at such a rate that the internal temperature did not go over10° C. as measured with an internal thermocouple probe. Once theaddition was complete, the ice bath was removed and the mixture wasallowed to stir while warming to room temperature. Although certainadducts require additional heat and/or base to produce the cyclization,this example with 2,6-dichloropicolinic acid chloride cyclizedspontaneously such that after 5 hours of stirring at room temperature,compound A could be isolated by diluting the reaction mixture withwater, extraction with dichloromethane (2×150 ml) and drying theresulting organic phase with sodium sulfate. Purification by triturationwith diethyl ether yielded 2.71 g (76% based on ethyl2-(benzothiazol-2-yl)acetate) as fluffy beige crystals. ¹HNMR (CDCl₃,400 MHz) 9.55 (1H, d, 8.4 Hz), 8.86 (1H, d, 8.4 Hz), 7.77 (1H, dd, 7.6,1.2 Hz), 7.61 (1H, m), 7.56 (1H, d, 8.4 Hz), 7.49 (1H, m), 4.53 (2H, q,7.2 Hz), 1.50 (3H, t, 7.2 Hz) ¹³CNMR (CDCl₃, 100 MHz) 171.1, 167.4,163.1, 152.9, 148.4, 140.5, 137.7, 128.5, 127.8, 126.6, 123.1, 122.1,121.7, 120.5, 106.3, 62.0, 14.7 LCMS: 359.3 (M+H)⁺.

It is understood that the foregoing detailed description andaccompanying examples are merely illustrative, and are not to be takenas limitations upon the scope of the invention. Various changes andmodifications to the disclosed embodiments will be apparent to thoseskilled in the art. Such changes and modifications, including withoutlimitation those relating to the chemical structures, substituents,derivatives, intermediates, syntheses, formulations and/or methods ofuse of the invention, may be made without departing from the spirit andscope thereof. U.S. patents and publications referenced herein areincorporated by reference.

1. A method for preparing a compound having formula 1:

and pharmaceutically acceptable salts, esters and prodrugs thereof,wherein: A, V, and Z are independently H, halo, azido, R², CH₂R², SR²,OR² or NR¹R²; or wherein A and Z, or V and Z may form a carbocyclicring, heterocyclic ring, aryl or heteroaryl, each of which may beoptionally substituted and/or fused with a cyclic ring; W is NR¹R² orOR⁶ wherein R⁶ is a C₁₋₁₀ alkyl; X is NR¹; each R¹ is H or a C₁₋₆ alkyl;each R² is H, or a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl each optionallysubstituted with a halogen, one or more non-adjacent heteroatoms, acarbocyclic ring, a heterocyclic ring, an aryl or heteroaryl, whereineach ring is optionally substituted; R is a substituent at any positionon B; and is H, OR², amino, alkoxy, amido, halogen, cyano or aninorganic substituent; or R is C₁₋₆ alkyl, C₂₋₆ alkenyl, —CONHR¹, eachoptionally substituted by one or more non-adjacent heteroatoms; or twoadjacent R are linked to obtain a 5-6 membered optionally substitutedcarbocyclic or heterocyclic ring, optionally fused to an additionaloptionally substituted carbocyclic or heterocyclic ring; B is anoptionally substituted ring, which may be aromatic or nonaromatic, andmay be monocyclic or fused with a single or multiple ring, wherein saidsingle or multiple ring may optionally contain one or more heteroatoms;n is 0-6; or a compound having formula (2A) or (4A):

wherein n, V, Z, X, W, B and R are as defined in formula (1),comprising: contacting a compound having formula (6A), (6B) or (6C)

wherein each L and L¹ is a leaving group; and A, V, and Z are as definedin formula (1); with a compound having formula (7) or tautomers thereof

wherein n, X, B and R are as defined in formula (1); and W is OR⁶wherein R⁶ is a C₁₋₁₀ alkyl; or W is NR¹R², wherein R¹ and R² are asdefined in formula (1); wherein said compound having formula (6A), (6B)or (6C) is contacted with said compound having formula (7) or tautomersthereof in the presence of a base to produce a compound having formula(1), and optionally hydrolyzing said compound of formula (1).
 2. Themethod of claim 1, wherein each W in formula (1), (2A) or (4A) is OR⁶,and R⁶ is a C₁₋₆ alkyl.
 3. The method of claim 2, further comprising thestep of contacting said compound having formula (1), (2A) or (4A) withan amine of the formulaHNR¹—(CR¹ ₂)_(n)—NR³R⁴  (3) wherein R¹ and R³ are independently H orC₁₋₆ alkyl; n is 1-6; and R⁴ is H, a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyloptionally containing one or more non-adjacent heteroatoms selected fromN, O and S, and optionally substituted with a carbocyclic orheterocyclic ring; or R³ and R⁴ together with N may form an optionallysubstituted ring containing one or more N, O or S.
 4. The method ofclaim 3, wherein R³ and R⁴ together with N form an optionallysubstituted piperidine, pyrrolidine, piperazine, morpholine,thiomorpholine, imidazole, or aminothiadiazole.
 5. The method of claim2, further comprising the step of contacting said compound havingformula (1), (2A) or (4A) with an amine of the formula HNR¹R², providedsaid amine is not NH₃.
 6. The method of claim 5, wherein R¹ is H, and R²is a C₁₋₁₀ alkyl optionally substituted with a heteroatom, a C₃₋₆cycloalkyl, aryl or a 5-14 membered heterocyclic ring containing one ormore N, O or S; or R¹ and R² together with N may form an optionallysubstituted heterocyclic ring containing one or more N, O or S.
 7. Themethod of claim 6, wherein R² is a C₁₋₁₀ alkyl substituted withmorpholine, thiomorpholine, imidazole, aminothiadiazole, pyrrolidine,piperazine, pyridine or piperidine; or R¹ and R² together with N formpiperidine, pyrrolidine, piperazine, morpholine, thiomorpholine,imidazole, or aminothiadiazole.
 8. The method of claim 1, wherein B ineach formula in claim 1 is an optionally substituted phenyl.
 9. Themethod of claim 1, wherein each R in each formula in claim 1 is H orhalo.
 10. The method of claim 1, wherein one of A and V is H or halo.11. The method of claim 10, wherein said halo is fluoro or chloro. 12.The method of claim 1, wherein each Z is H, halo, or SR² wherein R² isC₁₋₁₀ alkyl.
 13. The method of claim 1, wherein each L and L¹ is halo.14. The method of claim 1, comprising contacting said compound havingformula (6A), (6B) or (6C) and said compound having formula (7) to forma mixture, and contacting said mixture with said base.
 15. The method ofclaim 14, wherein said mixture is cooled to a temperature below roomtemperature, and contacting the base with said mixture.
 16. The methodof claim 14, wherein said base is contacted with said mixture at roomtemperature or at a temperature above room temperature.
 17. The methodof claim 1, wherein said base is an amine.
 18. The method of claim 17,wherein said amine is trialkylamine.
 19. The method of claim 1, whereinsaid compound having formula (6A), (6B) or (6C) is contacted with saidcompound having formula (7) to produce a compound having formula (4)

wherein n, W, V, A, Z, X, and R are as defined in formula (1) in claim1; formula (4B)

wherein n, W, V, Z, X, B and R are as defined in formula 1 in claim 1;or formula (5A)

wherein n, W, V, Z, X, and R are as defined in formula 1 in claim
 1. 20.The method of claim 1, wherein the compound having formula (6A), (6B) or(6C) is contacted with a compound of formula (7) or tautomers thereof inthe presence of a base and coordinating atom.
 21. The method of claim20, wherein said base has a pKa of less than
 20. 22. The method of claim20, wherein said base is triethylamine, diisopropyl ethyl amine,diazabicycloundecene, cesium carbonate,1,8-Bis(dimethylamino)naphthalene or dimethylamino pyridine (DMAP). 23.The method of claim 20, wherein said coordinating atom is thecoordinating metal of a Lewis acid.
 24. The method of claim 23, whereinsaid Lewis acid is has formula ML_(n), wherein L is a halogen atom or anorganic radical, n is 3-5, and M is a group II metal, group IIIelemental atom, a group IV elemental atom, As, Sb, V or Fe.
 25. Themethod of claim 23, wherein said group III elemental atom is B, orwherein said Lewis acid is MgCl₂.
 26. A method for preparing a compoundhaving formula (8)

wherein V, A, Z, and Y when attached to C are independently H, halo,azido, R², CH₂R², SR², OR², NR¹R²; or absent when attached to N; T¹, T²,T³, and T⁴ are independently C or N; W is NR¹R² or OR⁶, wherein R⁶ is aC₁₋₁₀ alkyl; X is NR¹; E together with N and X form a ring, which may befused with a single or multiple ring, wherein the single or multiplering optionally contains one or more heteroatoms; n is 1-6; p is 0-1;each R¹ is H or a C₁₋₆ alkyl; each R² is H, or a C₁₋₁₀ alkyl or C₂₋₁₀alkenyl each optionally substituted with a halogen, one or morenon-adjacent heteroatoms, a carbocyclic ring, a heterocyclic ring, anaryl or heteroaryl, wherein each ring is optionally substituted; R⁵ is asubstituent at any position on E; and is H, OR², amino, alkoxy, amido,halogen, cyano or an inorganic substituent; or R is C₁₋₆ alkyl, C₂₋₆alkenyl, —CONHR¹, each optionally substituted by one or morenon-adjacent heteroatoms; or two adjacent R are linked to obtain a 5-6membered optionally substituted carbocyclic or heterocyclic ring,optionally fused to an additional optionally substituted carbocyclic orheterocyclic ring; comprising contacting a compound having a formula (9)with a compound having formula (10) or tautomers thereof:

wherein n, p, V, A, Z, Y, T¹, T², T³, T⁴, X, W, E and R⁵ are as definedin formula (8); and each L and L¹ is a leaving group.
 27. The method ofclaim 26, wherein each L and L¹ is halo.
 28. The method of claim 26,comprising contacting said compound having formula (9) with saidcompound having formula (10) in the presence of a base.
 29. The methodof claim 26, wherein W is OR⁶ and R⁶ is a C₁₋₆ alkyl.
 30. The method ofclaim 26, wherein E is

wherein X is NR¹; X¹ and X² are independently CR¹ or NR¹; each R¹ is Hor C₁₋₆ alkyl.
 31. The method of claim 26, wherein each T¹, T², T³, andT⁴ is C.
 32. The method of claim 26, wherein T¹ is N, and each T², T³,and T⁴ is C.
 33. The method of claim 26, wherein T² is N, and each T¹,T³, and T⁴ is C.
 34. The method of claim 26, wherein each T⁴ and T³ isN, and each T² and T⁴ is C.
 35. The method of claim 26, wherein each T¹and is N, and each T² and T³ is C.
 36. The method of claim 26, whereineach T¹, T², and T³ is C, and T is N.
 37. The method of claim 26,wherein each leaving group is independently halo, tosylate, alkylsulfonyl, carbonate, acetate, carbamate, trifluoroacetate, phosphate,methoxy, activated methoxy, nitro, boron, or a substituted boron. 38.The method of claim 26, wherein said compound has formula (11)

and pharmaceutically acceptable salts, esters and prodrugs thereof;wherein V, X, and Y are absent if attached to a heteroatom other thanNitrogen, and independently H, halo, azido, R², CH₂R², SR², OR² or NR¹R²when attached to C or N; or wherein V and X, or X and Y may form acarbocyclic ring, heterocyclic ring, aryl or heteroaryl, each of whichmay be optionally substituted and/or fused with a cyclic ring; Z¹, Z²and Z³ are C, N, O or S; Z is NR²; E together with N and Z forms anoptionally substituted 5- or 6-membered ring that is fused to anoptionally substituted aryl or heteroaryl, wherein said aryl orheteroaryl may be monocyclic or fused with a single or multiple ring,and wherein said single or multiple ring optionally contains one or moreheteroatoms; Ring T is an optionally substituted 5-membered ring; U isR², OR², NR¹R², NR¹—(CR¹ ₂)_(n)—NR³R⁴, SO₃R², SO₂NR¹R² or SO₂NR¹—(CR¹₂)_(n)—NR³R⁴; wherein in each NR¹R², R¹ and R² together with N may forman optionally substituted ring; in NR³R⁴, R³ and R⁴ together with N mayform an optionally substituted ring; R¹ and R³ are independently H orC₁₋₆ alkyl; each R² is H, or a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl eachoptionally substituted with a halogen, one or more non-adjacentheteroatoms selected from N, O and S, a carbocyclic ring, a heterocyclicring, an aryl or heteroaryl, wherein each ring is optionallysubstituted; or R² is an optionally substituted carbocyclic ring,heterocyclic ring, aryl or heteroaryl; or R² is COR¹ or S(O)_(x)R¹wherein x is 1-2; R⁴ is H, a C₁₋₁₀ alkyl or C₂₋₁₀ alkenyl optionallycontaining one or more non-adjacent heteroatoms selected from N, O andS, and optionally substituted with a carbocyclic or heterocyclic ring;or R³ and R⁴ together with N may form an optionally substituted ring;each R⁵ is a substituent at any position on W; and is H, OR², amino,alkoxy, amido, halogen, cyano or an inorganic substituent; or R⁵ is C₁₋₆alkyl, C₂₋₆ alkenyl, —CONHR¹, each optionally substituted by halo,carbonyl or one or more non-adjacent heteroatoms; or two adjacent R⁵ arelinked to obtain a 5-6 membered optionally substituted carbocyclic orheterocyclic ring, optionally fused to an additional optionallysubstituted carbocyclic or heterocyclic ring; and n is 1-6.
 39. Themethod of claim 38, wherein ring T is selected from the group consistingof:

wherein V, X, Y and R² are as defined in formula (11).
 40. The method ofclaim 38, wherein said compound has formula (12A) or (12B)

wherein U, V, E, X, Y, Z, Z¹, Z², Z³, R⁵, T and n are as described informula (11); Z⁴ is CR⁶, NR², or C═O; and Z and Z⁴ may optionally form adouble bond.
 41. The method of claim 38, wherein said compound hasformula (13), (14) or (15)

wherein U, V, X, Y, Z, Z¹, Z², Z³, R⁵, T and n are as described informula (11).
 42. The method of claim 26, wherein the compound havingformula (9) is contacted with a compound of formula (10) or tautomersthereof in the presence of a base and coordinating atom.
 43. The methodof claim 42, wherein said base has a pKa of less than
 20. 44. The methodof claim 42, wherein said base is triethylamine, diisopropyl ethylamine, diazabicycloundecene, cesium carbonate,1,8-Bis(dimethylamino)naphthalene or dimethylamino pyridine (DMAP). 45.The method of claim 42, wherein said coordinating atom is thecoordinating metal of a Lewis acid.
 46. The method of claim 45, whereinsaid Lewis acid is has formula ML_(n), wherein L is a halogen atom or anorganic radical, n is 3-5, and M is a group II metal, group IIIelemental atom, a group IV elemental atom, As, Sb, V or Fe.
 47. Themethod of claim 45, wherein said group III elemental atom is B, orwherein said Lewis acid is MgCl₂.